Secondly, almost any Link would win with minimal effort, especially TP Link, who doesn't even use magic. The aforementioned Link's "Hidden Skills" aren't an implied result of magic either, and a good number of them show how much more agile Link actually is than Altair (I'd love to see Altair try to use the likes of the Helm Splitter or Back Slice). Link in general has virtually every physical advantage over Altair, having notable strength feats in TP even without any strength-enhancing items, and in general has three times as many weapons as Altair does. The only chance Altair has in this fight is if it's strictly a sword fight, and even then, he'd lose to at least 90% of the Links. Link could just use Mortal Draw the moment Altair lunges at him/comes within distance, and that'd the end of the monotone-suffering assassin.
Gameplaywise, maybe (not that Link would suffer from the same AI as the guards Altair often faces). But canonically, it won't make an ounce of difference. Taking into account sheer canoncal feats, Altair is nothing beyond a peak physical human who's skills are as such. Link has shown feats that, once again, borderline slightly beyond peak physical human, with a good enough record list that blows Altair's out of the water. To honestly say that Altair would last against the likes of Volvagia (who OOT Link was generally considered to have fought with only a hammer) or even a Darknut, is just blasphemy. Altair's never even faced anything beyond his own species. Even in a forseback duel, Link's got a bretter chance of winning, having taken on dozens of boar-riding marauders singlehandedly on at least two occasions singlegandedly, as well as taken on a camp full of beastly grunts whose numbers would require Altair to, gameplaywise, make an escape.
If you give them all their weapons, its a curbstomp in just about any Link's favor. If you give them only their swords, the only difference is Link not having as many weapons, but still winning without much trouble.
Well Link in TP was strong enough to lift a 20 ton Goron and toss it, and physically rivaled Ganondorf himself. And in OoT with the Golden Gauntlets he lifted and tossed that HUGE slag of what appeared to be a large black stone. And in WW, he tosses 10-15 tons boulders pretty easily.
Counter attacks? What stops Link from cutting through Altair's sword and killing Altair in the process?
He'll be slashing at air because Link is still more agile than him in fighting. Not that he would even be able to dodge the likes of the Back Slice or Helm Splitter.
Don't get me wrong, Altair is the shit, peak human physically most likely, and definately among the most skilled characters in gaming, but Altair cannot fvck with Link's raw physical strength, speed, power, and versatility. Not to mention he has pure martial skill to back it up.
To risk going off topic: About 2/3 right. Link's no hardcore burly badass but classifying him as if he were a JRPG protagonist (when the only matching asset he has is blue eyes in his more realistic incarnations) like you are is just needless exertion of ignorance and idiotic generalizing. Either way, no amount of queerness would hinder Link in this fight; his feats in TP put him on a level virtually 100% beyond Altair. Altair's good for what he is, but there are other (generally)normal humans who'd outdo him more easily than Link would.